requires made relative
make fasta-->plain coverter more convenient to use
genome folder made configurable in GeneDataLoader
remove notification about Sequence class from src (it's already in ToDo)
readability improved
move script to postprocessing
made tissue filtering a bit more readable
added class Mapping (not yet used)
hgnc_entrez mapping now find appropriate columns automatically (so different protein_coding_genes.txt formats are possible)
fixed error in mapping, added ability to find ambiguities
ability to load hgnc-entrez as Mapping instance
Mapping#unambigous? removed; ambigous hgnc-entrez mappings now raises exceptions
log about missing mapping pairs
hgnc_entrezgene mapping now works only with Mapping instances
mapping now can check ambiguity from different sides
entrez-->ucsc mapping also replaced with Mapping instance
fix ambiguities to be in better format
hgnc_entrez mapping file and gene infos by hgnc are the same file but really it can be done with different files, so separate variables
remove unnecessary fields from gene, added ensembl_id. Make gene loading independent from column order and presence
GeneDataLoader initialization now just save filenames etc, real work is done in #setup! logger can be set with GeneDataLoader#logger= and Gene.logger=. It's not global (but for Gene class is class instance-variable) now. LoggerStub is logger by default (with no output). Check for duplicates moved from read_hgnc_entrezgene_mapping to GeneDataLoader#setup!